Light vortex: Circularly polarized luminescence from a stirred and gelled solution of dye

If you hold one end of a rope and swing it up and down with your arm while the other end is tied to a fence, the rope forms a wave. The amplitude oscillates vertically. If you swing the rope left and right instead, the it oscillates horizontally. If the rope runs through a narrow gap between two trees, only the vertical wave can pass through to the end of the rope. Light can also be viewed as a wave.

The oscillation of ordinary light from a light bulb has no preferred direction. It varies in all directions perpendicular to the direction of propagation of the light. As the two trees do with the rope, special glasses, known as polarizing filters, allow only those light waves which oscillate in a specific plane to pass through. The light that passes through is known as linearly polarized light. Another variation is also possible: circularly polarized light. In this case, the light wave oscillates in a helical pattern because the amplitude describes a circle around the axis of propagation. The amplitude can rotate around to the left or the right.

The shape and orientation of molecules can influence the polarization plane of light when it passes through a given substance. It is thus not surprising that some molecules that emit light (luminesce) can give off polarized light. This luminescence can be circularly polarized if the emitting molecules (luminophores) are arranged helically.

The Japanese researchers from the Tokyo University of Science and the Nara Institute of Science and Technology have now found a new twist for emitting circularly polarized light: simply stir. Why does this work? Stirring causes spiral vortexes to form in liquids, which can induce the luminophores to adopt a helical arrangement.

The researchers were even able to preserve the forcibly twisted directionality of the luminescence by causing the solution containing the luminophore molecules, a green rhodamine dye, to gel while being stirred. A gel is formed like the gelatine glaze on a cake. Below a certain temperature the molecules of a gelling agent form a loose network with cavities that contain the other components of the liquid. If the dye solution with a suitable gelling agent is cooled under stirring, the stir-induced spiral arrangement of the luminophores is maintained in the gel. Depending on the direction of stirring, the gel emits left- or right-polarized luminescence. Without stirring, the light emitted is not polarized.

More information: Kunihiko Okano, Circularly Polarized Luminescence of Rhodamine B in a Supramolecular Chiral Medium Formed by a Vortex Flow, Angewandte Chemie International Edition, Permalink to the article: http://dx.doi.org/ … ie.201104708

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Scientists develop the most advanced computer model to-date of the scattering of polarized light from chiral molecules

An international research team has described the first calculations of Raman optical activity (ROA) spectra using coupled-cluster theory – one of the most reliable quantum chemical methods available. ROA is a valuable tool for the structural characterization of a wide range of molecules, including large biomolecules such as viruses and proteins for which the technique holds a particular prominence.

“We have developed the most advanced computer model to-date of the scattering of polarized light from chiral molecules”, says T. Daniel Crawford, researcher at Virginia Tech (USA), who carried out the simulations together with Kenneth Ruud of the University of Tromso (Norway). Chirality – or handedness – is a very important property in chemistry. The new results are presented in the journal ChemPhysChem.

A long-term goal of this area of research is to enable laboratory chemists to carry out their own simulations to study compounds ranging from small molecules to pharmaceuticals and viruses. “This will allow them to identify which ‘hand’ of the compound reacts in a desired way –from providing a certain scent to fighting tumors”, Crawford says. He points out that the model developed by him and his Norwegian colleague is capable of providing predictions of many molecular properties that equal –and sometimes exceed– the accuracy of even the best available experiments. Besides describing the fundamental theoretical aspects of the coupled-cluster functions used in the calculation of ROA spectra, Crawford and Ruud have demonstrated the effectiveness of their method through benchmark computations on (S)-methyloxirane –a compound for which experimental gas-phase data are available. Such rare experimental data, which are free of perturbative solvent effects, provide an excellent testing ground for advanced quantum-chemical methods.

According to the researchers, their future work will focus on more systematic comparisons between coupled-cluster ROA spectra and both density functional theory (DFT) and experiment, including more molecular examples. “Ultimately, we and the world's other quantum chemists seek to carry out ‘computational experiments’ that will provide reliable data more quickly, more safely, and with less expense than laboratory analyses”, Crawford adds.

More information: Daniel Crawford, Coupled-Cluster Calculations of Vibrational Raman Optical Activity Spectra, ChemPhysChem, Permalink to the article: http://dx.doi.org/ … hc.201100547

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Polarized microscopy technique shows new details of how proteins are arranged

Whether you're talking about genes, or neurons, or the workings of a virus, at the most fundamental level, biology is a matter of proteins. So understanding what protein complexes look like and how they operate is the key to figuring out what makes cells tick. By harnessing the unique properties of polarized light, Rockefeller scientists have now developed a new technique that can help deduce the orientation of specific proteins within the cell. By turning their instruments toward the nuclear pore complex, a huge cluster of proteins that serves as a gateway to a cell's nucleus, the scientists say they have filled in the gaps left by other techniques and made important new discoveries about how the complex works.

"Our new technique allows us to measure how components of large protein complexes are arranged in relation to one another," says Sandy Simon, head of the Laboratory of Cellular Biophysics. "This has the potential to give us important new information about how the nuclear pore complex functions, but we believe it can also be applied to other multi-protein complexes such as those involved in DNA transcription, protein synthesis or viral replication."

Although researchers have spent years studying the workings of the nuclear pore complex, there is still much that has remained mysterious. One problem is that there is a "resolution gap" between the two techniques primarily used to visualize protein complexes. Electron microscopy can reveal the broad outlines of a large protein complex, but it can't show details. X-ray crystallography, meanwhile, can show minute detail but only of a small piece of the complex; it can't say how the individual pieces fit together. To further complicate matters, both techniques require fixed samples – while they can give you an idea of what something looks like at a moment in time, they can't tell you how its pieces might move.

The new technique was developed by Simon along with postdoc Alexa Mattheyses, graduate student Claire Atkinson and Martin Kampmann, a former a member of Günter Blobel's Laboratory of Cell Biology who is currently at the University of California, San Francisco. It takes advantage of the properties of polarized light to show how specific proteins are aligned in relation to one another. After genetically attaching fluorescent markers to individual components of the nuclear pore complex, the scientists replaced the cell's own copy of the gene that encodes the protein with the new form that has the fluorescent tag. Then, they used customized microscopes to measure the orientation of the waves of light the fluorescently tagged proteins emitted. By combining these measurements with known data about the structure of the complex, the scientists can confirm or deny the accuracy of previously suggested models.

"Our experimental approach to the structure is synergistic with other studies being conducted at Rockefeller, including analysis with X-ray crystallography in Günter's lab and electron microscopy and computer analysis in Mike Rout's lab," says Simon. "By utilizing multiple techniques, we are able to get a more precise picture of these complexes than has ever been possible before."

The scientists used the technique to study nuclear pore complexes in both budding yeast and human cells. In the case of the human cells, their new data shows that multiple copies of a key building block of the nuclear pore complex, the Y-shaped subcomplex, are arranged head-to-tail, rather than like fence posts, confirming a model proposed by Blobel in 2007.

"As a graduate student with Günter Blobel, I determined the three-dimensional structure of the Y-shaped subcomplex using electron microscopy," says Kampmann. "However, it was still a mystery how these 'Y's are arranged. The new technique we have developed reveals the orientation of building blocks in the cell, and we hope that it will eventually enable us to assemble individual crystal structures into a high-resolution map of the entire nuclear pore complex."

Eventually, the scientists say their technique could go even further. Because the proteins' fluorescence can be measured while the cells are still alive, it could give scientists new insights into how protein complexes react to varying environmental conditions, and how their configurations change over time.

"What happens when other proteins pass through the nuclear pore? Does the orientation of the nucleoporins change? With this technique, can find out not only what the pore looks like when it's sitting still, but what happens to it when it's active," Simon says. Their first characterization of the dynamics of the nuclear pore proteins was published recently in The Biophysical Journal.

Provided by Rockefeller University (news : web)